openforcefield · mattwthompson · Jan 6, 2025 · Jan 6, 2025 · Jan 6, 2025 · Jan 6, 2025
diff --git a/.github/workflows/hugo.yml b/.github/workflows/hugo.yml
@@ -34,7 +34,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     env:
-      HUGO_VERSION: 0.108.0
+      HUGO_VERSION: 0.140.0
     steps:
       - name: Install Hugo CLI
         run: |

diff --git a/config.toml b/config.toml
@@ -6,17 +6,22 @@ theme = "openff"
 enableEmoji = true
 
 [markup]
-  defaultMarkdownHandler = "goldmark"
   [markup.goldmark]
     [markup.goldmark.renderer]
       unsafe = true
-
+    [markup.goldmark.extensions]
+      [markup.goldmark.extensions.passthrough]
+        enable = true
+        [markup.goldmark.extensions.passthrough.delimiters]
+          block = [['\[', '\]'], ['$$', '$$']]
+          inline = [['\(', '\)']]
 [params]
   header_title = "<b>open</b> force field"
   header_subtitle = "An open and collaborative approach to better force fields"
   "cc-by-4.0" = "https://creativecommons.org/licenses/by/4.0/"
   "cc-by-nc-nd-4.0" = "https://creativecommons.org/licenses/by/4.0/"
   "arxiv-1.0" = "https://arxiv.org/licenses/nonexclusive-distrib/1.0/license.html"
+  math = true
 
 [menu]
 

diff --git a/content/community/news/general/benchmark-small-molecules/index.md b/content/community/news/general/benchmark-small-molecules/index.md
@@ -8,7 +8,6 @@ draft: false
 description: 'Force Field benchmark on small molecule energies and geometries.'
 weight: 10
 author: "David Hahn"
-markup: mmark # mmark is necessary for LaTeX to work properly
 thumb: benchmark-small-molecules.png
 ---
 

diff --git a/content/community/news/general/introducing-openforcefield-1.0/index.md b/content/community/news/general/introducing-openforcefield-1.0/index.md
@@ -8,7 +8,6 @@ draft: false
 description: 'At the end of our first year, the Open Force Field Consortium releases its first optimized force field: the Open Force Field 1.0 (codename "Parsley") small molecule force field'
 weight: 10
 author: "David Mobley, Yudong Qiu, Simon Boothroyd, Lee-Ping Wang, and John Chodera"
-markup: mmark # mmark is necessary for LaTeX to work properly
 thumb: "noun_parsley.svg"
 ---
 

diff --git a/content/community/news/general/openforcefield-toolkit-0.2-release.md b/content/community/news/general/openforcefield-toolkit-0.2-release.md
@@ -5,7 +5,6 @@ tags: ["news","general","OpenFF Toolkit", "cheminformatics","SMIRNOFF", "softwar
 categories: ["news"]
 draft: false
 description: "Release of major new toolkit version, with open-source cheminformatics support."
-markup: mmark
 weight: 10
 author: "Jeff Wagner"
 thumb: "rdkit-logo.jpg"

diff --git a/content/community/news/general/openforcefield-toolkit-0.5-release.md b/content/community/news/general/openforcefield-toolkit-0.5-release.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "OpenFF Toolkit", "GBSA", "SMIRNOFF", "cheminformatics
 categories: ["news"]
 draft: false
 description: "Major OFF Toolkit milestone, adding support for implicit solvation."
-markup: mmark
 weight: 10
 author: "Jeff Wagner"
 thumb: "openff-toolkit-logo.jpg"

diff --git a/content/community/news/general/rdkit-support-is-coming.md b/content/community/news/general/rdkit-support-is-coming.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "OpenFF Toolkit", "cheminformatics", "RDKit", "OpenEye
 categories: ["news"]
 draft: false
 description: "A rundown of coming changes and improvements in the openforcefield toolkit."
-markup: mmark
 weight: 10
 author: "John Chodera"
 thumb: "openff-toolkit-logo.jpg"

diff --git a/content/community/news/general/seeking-nih-funding/index.md b/content/community/news/general/seeking-nih-funding/index.md
@@ -5,7 +5,6 @@ tags: ["news","general","Open Force Field Initiative", "NIH", "funding"]
 categories: ["news"]
 draft: false
 description: "The Open Force Field Initiative has applied for NIH R&D funding to produce modern toolkits and high-quality biomolecular force fields to model complex heterogeneous biomolecular systems"
-markup: mmark
 weight: 10
 author: "John Chodera"
 thumb: "openff-nih-funding.png"

diff --git a/content/community/news/general/webinar-daga-sep2019.md b/content/community/news/general/webinar-daga-sep2019.md
@@ -5,7 +5,7 @@ tags: ["news","general", "Pankaj R. Daga", "webinar","data curation", "AI", "dru
 categories: ["news"]
 draft: false
 description: "Pankaj R. Daga will give a talk at UC Irvine on Sep 13 at 11 am (PT) about importance of data curation in the age of AI"
-markup: mark
+markup: markdown
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-daga-sep2019.jpg"

diff --git a/content/community/news/general/webinar-gapsys-aug2019.md b/content/community/news/general/webinar-gapsys-aug2019.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "Vytautas Gapsys", "webinar","benchmarking", "binding
 categories: ["news"]
 draft: false
 description: "Vytautas Gapsys will give a talk at UC Irvine on Aug 21 at 11 am (PT) on his work on binding free energy calculations."
-markup: mmark
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-gapsys-aug2019.png"

diff --git a/content/community/news/general/webinar-hoffman-sep2019.md b/content/community/news/general/webinar-hoffman-sep2019.md
@@ -5,7 +5,7 @@ tags: ["news", "general", "Falk Hoffmann", "CHARMM","AMBER", "force field", "NMR
 categories: ["news"]
 draft: false
 description: "Falk Hoffmann will give a webinar on Sep 20 at 11 am (EDT) about his recent study on methyl group dynamics in amino acid side-chains using MD simulations and NMR relaxation rates"
-markup: mark
+markup: markdown
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-hoffman-sep2019.png"

diff --git a/content/community/news/general/webinar-kraemer-dec2019.md b/content/community/news/general/webinar-kraemer-dec2019.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "Andreas Krämer", "webinar","CHARMM", "force field",
 categories: ["news"]
 draft: false
 description: "Andreas Krämer will talk about automated optimization of the CHARMM36 lipid force field on Dec 17 at 2 pm (ET)."
-markup: mmark
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-kraemer-dec2019.png"

diff --git a/content/community/news/general/webinar-stern-may2019.md b/content/community/news/general/webinar-stern-may2019.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "Chaya Stern", "webinar","torsions", "fragmentation",
 categories: ["news"]
 draft: false
 description: "Chaya Stern gives a webinar about her work done on molecular fragmentation and torsion drive pipeline on Jun 4 at 11 am (EDT)"
-markup: mmark
 weight: 10
 author: "Karmen Condic-Jurkic and Chaya Stern"
 thumb: "webinar-stern-may2019.jpg"

diff --git a/content/community/news/general/webinar-tian-sep2019.md b/content/community/news/general/webinar-tian-sep2019.md
@@ -5,7 +5,7 @@ tags: ["news", "general", "Chuan Tian", "webinar","Amber", "force field", "ff19S
 categories: ["news"]
 draft: false
 description: "Chuan Tian presents his work on the latest version of Amber force field (ff19SB) at 1 pm (ET) on Sep 12"
-markup: mark
+markup: markdown
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-tian-sep2019.jpg"

diff --git a/content/community/news/general/webinar-wang-oct2019.md b/content/community/news/general/webinar-wang-oct2019.md
@@ -5,7 +5,6 @@ tags: ["news", "general", "Yuanqing Wang", "webinar","Graph Nets", "machine lear
 categories: ["news"]
 draft: false
 description: "Yuanqing Wang (MSKCC) will talk about his ongoing work on applying machine learning techniques for fast prediction of atomic charges on Oct 14 at 1 pm (ET)."
-markup: mmark
 weight: 10
 author: "Karmen Condic-Jurkic"
 thumb: "webinar-wang-oct2019.png"

diff --git a/content/manual/_index.md b/content/manual/_index.md
@@ -318,9 +318,6 @@ Also it has its own header:
 - author: "David Mobley, Yudong Qiu, Simon Boothroyd, Lee-Ping Wang, and John Chodera"{{< br >}}
 *Authors of the item*
 
-- markup: mmark # mmark is necessary for LaTeX to work properly{{< br >}}
-*For use of markdown with LaTeX*
-
 - thumb: "5-The-Open-Force-Field-1.0-small-molecule-force-field,-our-first-optimized-force-field-(codename-_Parsley_).jpg"{{< br >}}
 *Thumb image used with the item, the images are in the same folder as the items*
 {{< br >}}{{< br >}}

diff --git a/content/math-examples.md b/content/math-examples.md
@@ -0,0 +1,21 @@
+This is an inline \(a^*=x-b^*\) equation.
+
+These are block equations:
+
+\[a^*=x-b^*\]
+
+\[ a^*=x-b^* \]
+
+\[
+a^*=x-b^*
+\]
+
+These are also block equations:
+
+$$a^*=x-b^*$$
+
+$$ a^*=x-b^* $$
+
+$$
+a^*=x-b^*
+$$
diff --git a/themes/openff/layouts/_default/baseof.html b/themes/openff/layouts/_default/baseof.html
@@ -14,6 +14,9 @@
 	{{ with .Site.Params.description }}<meta name="description" content="{{ . }}">{{ end }}
 	{{ with .Site.Params.author }}<meta name="author" content="{{ . }}">{{ end }}
 	{{ $style := resources.Get "sass/index.scss" | toCSS | minify | fingerprint }}
+    {{ if .Param "math" }}
+      {{ partialCached "math.html" . }}
+    {{ end }}
 	<link rel="stylesheet" href="{{ $style.Permalink }}">
 	{{ with .OutputFormats.Get "RSS" -}}
 		{{ printf `<link rel="%s" type="%s" href="%s" title="%s">` .Rel .MediaType.Type .RelPermalink $.Site.Title | safeHTML }}

diff --git a/themes/openff/layouts/partials/math.html b/themes/openff/layouts/partials/math.html
@@ -0,0 +1,9 @@
+<script id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js"></script>
+<script>
+  MathJax = {
+    tex: {
+      displayMath: [['\\[', '\\]'], ['$$', '$$']],  // block
+      inlineMath: [['\\(', '\\)']]                  // inline
+    }
+  };
+</script>